The bio-objects project. Part I: the object data model core elements.

MOTIVATION: Scientific data reside in a number of different data sources, both public and commercial, and are accessible through various software applications. Data and software interoperability is becoming a critical issue in the research community. In our opinion, the need to develop a unified object model for biotechnology must be recognized. Herein, we present a prototype and core elements for the Object Data Model, a central part of our future commercial product development. RESULTS: We have designed a first layer of the Object Data Model that will be used for further commercial application development. The CBioBase object was designed as a citable, stable and core data element for the Object Data Model. General relationships between objects and application components were established. AVAILABILITY: Software tools will be provided with a future DNASIS product to access various elements of the Object Model. We are planning to assemble C++ libraries and Java binary files into BioObjects SDK (software development kit) for those interested in software implementation using the described object model. CONTACT: smaltch@msn.com or smaltch@hitachi-soft.com

Cruciform-extruding regulatory element controls cell-specific activity of the tyrosine hydroxylase gene promoter.

Tyrosine hydroxylase (TH) is expressed specifically in catecholaminergic cells. We have identified a novel regulatory sequence in the upstream region of the bovine TH gene promoter formed by a dyad symmetry element (DSE1;-352/-307 bp). DSE1 supports TH promoter activity in TH-expressing bovine adrenal medulla chromaffin (BAMC) cells and inhibits promoter activity in non-expressing TE671 cells. DNase I footprinting of relaxed TH promoter DNA showed weak binding of nuclear BAMC cell proteins to a short sequence in the right DSE1 arm. In BAMC cells, deletion of the right arm markedly reduced the expression of luciferase from the TH promoter. However, deletion of the left DSE1 arm or its reversed orientation (RevL) also inactivated the TH promoter. In supercoiled TH promoter, DSE1 assumes a cruciform-like conformation i.e., it binds cruciform-specific 2D3 antibody, and S1 nuclease-cleavage and OsO4-modification assays have identified an imperfect cruciform extruded by the DSE1. DNase I footprinting of supercoiled plasmid showed that cruciformed DSE1 is targeted by nuclear proteins more efficiently than the linear duplex isomer and that the protected site encompasses the left arm and center of DSE1. Our results suggest that the disruption of intrastrand base-pairing preventing cruciform formation and protein binding to DSE1 is responsible for its inactivation in DSE1 mutants. DSE1 cruciform may act as a target site for activator (BAMC cells) and repressor (TE671) proteins. Its extrusion emerges as a novel mechanism that controls cell-specific promoter activity.